\Header{visualiseHybridisations}{Microarray intensity data are visualised with respect
to their spatial layout}
\keyword{hplot}{visualiseHybridisations}
\begin{Description}\relax
Two colour microarray intensity data are visualised
with respect to their spatial layout.
Missing values (\code{NA}) as well as
minus infinity (\code{-Inf})
etc. are not visualised.
They appear to be white, i.e. in the colour of the background.
\code{-Inf} might be a result of the (log-)transformation
of the data; cf. the argument \code{transFunc}.
\end{Description}
\begin{Usage}
\begin{verbatim}visualiseHybridisations(arrayDataObject, exprSetRGObject, type="raw", hybridisations, slideNameColumn, numberOfSpots, nrOfBlocksPerRow=4, mappingColumns= list(Block="Block", Column="Column", Row="Row"), transFunc=log, savePath=".", plotOutput="pdf")\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{arrayDataObject}] object of class \code{\Link{arrayData}};
required; default: missing
\item[\code{exprSetRGObject}] object of class \code{\Link{exprSetRG}};
only required,
if \code{type = "normalised"} or
\code{type = "normalisedLogRatio"};
default: missing
\item[\code{type}] vector of character strings; required; default "raw";
valid strings are "raw", "rawLogRatio",
"rawLogRatioBackgroundSubtracted", "normalised"
or "normalisedLogRatio"
\item[\code{hybridisations}] vector of integers; optional; default: missing,
i.e. all microarray slides
\item[\code{slideNameColumn}] character string specifying the column
\code{getHybAttr(arrayDataObject)}
which contains the names
of the hybridisations; optional;
default: missing
\item[\code{numberOfSpots}] integer; optional; default: missing;
but required if the values in \code{arrayDataObject}
do not cover the whole microarray slide, i.e.
do not contain all spots;
cf. \code{\Link{spatialLayout}}.
\item[\code{nrOfBlocksPerRow}] integer; cf. \code{\Link{spatialLayout}};
required; default: 4
\item[\code{mappingColumns}] list; required; the list elements named
"Block", "Column", "Row" define the
corresponding column names given in
\code{getSpotAttr(arrayDataObject)};
the "Block" element is optional, if
missing a single block is assumed;
default: \code{list(Block="Block",
                        Column="Column", Row="Row")};
cf. \code{\Link{spatialLayout}}

\item[\code{transFunc}] transformation function
applied to the raw data,
in particular in combination with \code{type = "raw"}
you may for example use \code{log} or \code{rank};
(note: \code{type = "rawLogRatio"} and
\code{type = "rawLogRatioBackgroundSubtracted"}
require log );
required; default: log
\item[\code{savePath}] character string; required; default: "."
\item[\code{plotOutput}] character string; required; either "screen", "pdf"
or "win.metafile"; default: "pdf"
\end{ldescription}
\end{Arguments}
\begin{Value}
None, but a plot is generated.
\end{Value}
\begin{Author}\relax
Andreas Buness <a.buness@dkfz.de>
\end{Author}
\begin{SeeAlso}\relax
\code{\Link{spatialLayout}},
\code{\Link{exprSetRG-class}},
\code{\Link{arrayData-class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
        \end{ExampleCode}
\end{Examples}

